GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Azohydromonas australica DSM 1124

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_029000246.1 H537_RS0126340 D-glycerate dehydrogenase

Query= curated2:Q9YAW4
         (335 letters)



>NCBI__GCF_000430725.1:WP_029000246.1
          Length = 323

 Score =  202 bits (515), Expect = 7e-57
 Identities = 128/320 (40%), Positives = 178/320 (55%), Gaps = 6/320 (1%)

Query: 1   MKRPRVFVTREVFPEALELLSKYYDVEVWDKYQPPPYETLLSKAREADALYTLLTDRIDC 60
           M R  V V R + P+ L  +++ +DV V D  +    +  L    +A  L    +  +D 
Sbjct: 1   MNRKNVVVFRALPPDLLARITERHDVVVADPRRTEERQRFLDALPQAQGLIGS-SFALDA 59

Query: 61  DLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRV 120
             L +AP L +++ ++VG DN ++    R GI + NTPGVLTE TA+  +ALIL A+RR+
Sbjct: 60  QTLDRAPALEVISSISVGVDNYELPYLERRGITLCNTPGVLTETTADTLFALILCASRRL 119

Query: 121 VEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAE-IGKAFGMRIIY 179
           VE  + VR G W R   G     + G ++ GKTLGILG GRIG  +A      FGM ++Y
Sbjct: 120 VELSNLVREGRWTR-NIGED---LFGWDVHGKTLGILGFGRIGQALARRAALGFGMPVLY 175

Query: 180 HSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVN 239
           H     R  E         ++++L+ +DI+++ LPL++ TR L+G  E  LMK  AI VN
Sbjct: 176 HDPFEVRVPELSGLVTRLPMDEVLQRADIVALTLPLSEATRGLMGAREFALMKSGAIFVN 235

Query: 240 TGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETR 299
             RG +V   AL++AL  G + AAALDVF  EPL    PL     V   PH  SAT ETR
Sbjct: 236 GARGGLVQEDALLQALDNGPLRAAALDVFATEPLPQASPLRTHPRVTPLPHIGSATHETR 295

Query: 300 LRMAMMAAENLVAFAQGKVP 319
             MA +A ENL+A   G+ P
Sbjct: 296 RAMAELATENLLAVLDGEPP 315


Lambda     K      H
   0.322    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 253
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 335
Length of database: 323
Length adjustment: 28
Effective length of query: 307
Effective length of database: 295
Effective search space:    90565
Effective search space used:    90565
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory